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Jean Grey gives a talk to Senate, urging against Mutant registration. She is mocked and shown up by one Senator Kelly.
Logan encounters Rogue, agrees to give her a ride.
Sabretooth ambushes the vehicle, rendering Logan temporarily unconscious before Storm and Cyclops arrived to rescue both Logan and Rogue.

Logan awakes in the medlab, shortly after to meet Xavier and the rest of his X-men team, and Xavier convinces Logan to give him two days to try and discover why Magneto sent Sabretooth after him.

That night, Rogue hears Logan having a nightmare, and in attempting to waken him, ends up impaled on his claws. In an attempt to save herself, she touches him, leaving him having seizure when the three X-men arrive.
The following day, Mystique disguised as Bobby convinces Rogue to run away from the mansion, leading her to believe Professor Xavier is angry with her for using her powers on Logan. Logan discovers she's missing, and Xavier uses Cerebro to discover she is at the train station. Xavier dispatches Cyclops and Storm to retrieve her, but Logan sneaks out on Scott's motorcycle in an attempt to bring her back himself. Meanwhile, Mystique uses her powers of metamorphisis to infiltrate Cerebro to sabotage it.
Instead of a smooth recovery of Rogue, the X-men wander into an ambush of Magneto and his Brotherhood, resulting in heavy damage to the train station, Logan being manipulated and knocked out by Magneto, and Rogue being kidnapped.

Returning to the mansion, Logan intends to leave to look for Rogue himself, and discovers an ailing Senator Kelly at the mansion door. Xavier enters Kelly's mind, discovering Magneto's attempt to mutate the senator, and that the machine he uses to do so weakens Magneto greatly. While rehashing this information with the others, they hit upon the purpose Magneto has taken Rogue : He intends to transfer his power to her, and use her to power the machine, careless of whether or not she'll survive. Shortly after this discovery, Storm delivers the news that Senator Kelly has died.

Xavier attempts to use Cerebro to locate Rogue in order to rescue her. Mystique's sabotage works, sending the Professor into a mental comatose state. While the others are attending to Xavier and other things, Jean discovers Mystique's handiwork and undoes it, restoring Cerebro. Heedless of the danger to herself, Jean uses Cerebro, discovering Magneto's destination.

The X-men use the jet to fly to Liberty Island, where Magneto has installed his machine in the torch in order to use it to mutate the world leaders meeting on nearby Ellis Island. After battling Toad, Mystique, and Sabretooth, the X-men realize Magento has already touched Rogue and transferred his power to her, leaving her helpless to stop the machine.

Logan allows Storm and Jean to launch him airborne to try and get atop the machine and stop it, before it mutates everyone on Ellis Island and kills Rogue. Magneto uses his powers to stop Logan's claws from freeing Rogue, until Scott uses his concussive beams to put Magneto down.

At first, it seems that though the city is safe, Rogue has paid for Magneto's plan. Logan attempts to use her skin's power to draw in his healing to revive her. After what seems to be failure, Rogue's powers flare, and she heavily drains Logan's regenerative powers, having to push him away from her to stop herself from killing him.

In the aftermath, Magneto is arrested and kept in a plastic prison. Xavier and Logan both eventually awaken back at the mansion, well and able. Xavier tells Logan where to find an old military complex that may have some answers. Logan then leaves the mansion, but with a promise to Rogue that he will return.